Controlling armature through python
I'm afraid dynamically changing the mesh connected to the armature is not possible inside the Blender game engine without implementing it as a new feature in the source code. 

All deformations of meshes must either be done vertex by vertex or through actions in the Dope sheet editor.

If you create action logic bricks that correspond to the limb movement you are trying to get to work, you should be able to get limited model deformation movements going. Changing an action actuator's start and end frames is possible when the game engine is running. This gives you some of the control you seek.